SpikeGLX
Highlights, hints and tips
UCL Course 10/14/2024
Resources (all free, open source)
•Download page, it’s all here: https://billkarsh.github.io/SpikeGLX/
•Get the latest version: bug fixes, richest metadata
•Quick-ref: tour all the main features
•Videos
•Manuals and help documents
•Metadata Guides, Latest items:
•GeomMaps
•Tip Length
•Anatomy
•Probe error flags
•Mux Table (helps 3rd-party software do multiplexing time-shift corrections)
Metadata complete: Everything you need to know about THIS probe is in there…
3rd-party processing tools don’t need tables of auxiliary data.
Probe Geometry (Metadata ~snsGeomMap)
Z=0
tip length
X=0
X=0
X=0
X=0
width
shank spacing
Z
X
•Replaces ~snsShankMap.
•Gives locations of all selected sites on
the probe surface in microns.
•Uses coordinate system shown here.
This is described in ‘Metadata_30’ guide
How to Run
•New Acquisition (Ctrl+N)
•Configure dialog ->
•Data flow: Follow the tabs:
•Which hardware
•Hardware parameters
•Synchronizing the hardware
•How/when files are written
•Where to save data, what to call it
•Context help at each step
Where I plugged my probes,
Which {slot port dock}. NEW:
Slots can be PXI, OneBox, Sim.
All NI devices are here Help on current tab
? in title bar = more help
OneBox ! ?
•8 x 8 X 1 inches
•USB 3.0
•2 probe ports
•12 Aux analog channels in
•12 analog out
•~ 3600 EUR
•Order: Neuropixels.org
Quickstart Guide:
•SpikeGLX/_Help
•Online
Assign slot to each OneBox!
1. Add…
2. Browse for run file
3. Assign { slot port dock }, double-click the cells
4. Click Enable
Devices Tab
IM Setup Tab
•Lower latency remote fetching NEW!!
•Survey mode
•Check box, secs/bank
•FileViewer to see survey
•Filtered buffers NEW!!
•Check box, bandpass
•Better SNR:
•Audio
•ShankViewer
•SpikeViewer
•IMRO editor
•Double-click cell
See, context sensitive
1. Set rows/box
2. Set width {full, half} shank
3. Click to place centers of boxes
4. Resize; shift-click to remove box
5. When sum = rqd, save as a file
But this is much cooler
when you can see the
activity on the shank…
And you can:
1. Online in ShankViewer
2. Offline in FileViewer
ShankViewer Edit tab!!
IMRO Editor
Green boxes
select sites
for readout